percent homology after edited lineup ?

Jack Leunissen jackl at caos.kun.nl
Mon Aug 2 06:37:45 EST 1993

rherzog at dec5.ulb.ac.be (Robert Herzog) writes:

>Maybe I'm missing something trivial...
>We have been looking at how to obtain the percent identity between any pair of
>protein sequences that have been :
>1. aligned with pileup
>2. the alignment has been edited with lineup to "improve" it
>We used some hacking to get the result, but is there someone around who prepared
>a script/program/set of commands that performs this in a single or a few simple

I have written a program called HOMOLOGIES, which includes/supersedes GCG's
DISTANCES. It can calculate percentage identity, homology, or distances.
Gaps can be included or excluded. The distance-matrix can be saved in PHYLIP
format, to use it with FITCH or NEIGHBOR.

To obtain a copy, send mail to jackl at caos.kun.nl.


      Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center
      Email: jackl at caos.kun.nl   | University of Nijmegen
      Tel. : +31 80 65 22 48     | Toernooiveld 1
      Fax  : +31 80 65 29 77     | 6525 ED Nijmegen, The Netherlands
    +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+

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